Spike in (404) not founds, what to do?

Recently I setup a process for updating the website's inventory from our internal system, so a bunch of products have become no longer available. It's caused many URLs that Google had indexed to become 404 because, using the example URL above - we no longer have any men's large purple shirts. There are about 2000 of them.

I hate to see all these errors in the webmaster account, but it is accurate. Is there anything I should do? Is my site being penalized for a sudden spike in 404s? I feel strongly that Google would push my site lower on the SERPs due to a sudden spike in 404s, certainly it must appear like an unstable or poor quality site. I considered adding those URLs to my robots.txt as disallowed, then requesting their removal... but what if I get new merchandise with those same facets? How is something like this usually handled in ecommerce?

Thanks for the reply Vla. I'm not sure what you mean. "Manually" what? I use Google webmaster tools, and I can see all of the 404s. Since they're actually 404s, I don't intend to "Mark as Fixed" any of them.

Go to - Webmaster Tools - Optimization - Remove URL and after that mark as fixed
and remove them manually - one by one if are not hundreds or thousands

and your problem solved

After you do this -wait two-three days - create a new sitemap and submit it

Good luck

There is no need to remove them manually, as long as your sitemap is up to date either manually or through a CMS then there is no need to re-submit your sitemap as webmaster tools automatically scans the sitemap for any differences. Don't worry about the errors too much, especially with a site your size as you would probably be changing items/clothing on a regular basis so getting error messages would be common.

I would suggest creating a 404 error page so you can let customers know the product no longer exists with a link back to the home page perhaps or even setting up a general re-direct in .htaccess for all your dead pages (this is only a couple of lines and saves hours of work!), and it gives the spiders somewhere to point to when they have reached an error page.

Go to - Webmaster Tools - Optimization - Remove URL and after that mark as fixed
and remove them manually - one by one if are not hundreds or thousands

and your problem solved

After you do this -wait two-three days - create a new sitemap and submit it

Good luck

There is no need to remove them manually, as long as your sitemap is up to date either manually or through a CMS then there is no need to re-submit your sitemap as webmaster tools automatically scans the sitemap for any differences. Don't worry about the errors too much, especially with a site your size as you would probably be changing items/clothing on a regular basis so getting error messages would be common.

I would suggest creating a 404 error page so you can let customers know the product no longer exists with a link back to the home page perhaps or even setting up a general re-direct in .htaccess for all your dead pages (this is only a couple of lines and saves hours of work!), and it gives the spiders somewhere to point to when they have reached an error page.